Reproducibility-optimized test statistic for ranking genes in microarray studies

A principal goal of microarray studies is to identify the genes showing differential expression under distinct conditions. In such studies, the selection of an optimal test statistic is a crucial challenge, which depends on the type and amount of data under analysis. While previous studies on simulated or spike-in datasets do not provide practical guidance on how to choose the best method for a given real dataset, we introduce an enhanced reproducibility-optimization procedure, which enables the selection of a suitable gene- anking statistic directly from the data. In comparison with existing ranking methods, the reproducibilityoptimized statistic shows good performance consistently under various simulated conditions and on Affymetrix spike-in dataset. Further, the feasibility of the novel statistic is confirmed in a practical research setting using data from an in-house cDNA microarray study of asthma-related gene expression changes. These results suggest that the procedure facilitates the selection of an appropriate test statistic for a given dataset without relying on a priori assumptions, which may bias the findings and their interpretation. Moreover, the general reproducibilityoptimization procedure is not limited to detecting differential expression only but could be extended to a wide range of other applications as well.     

Identification of a set of genes involved in the biosynthesis of the aminonucleoside moiety of antibiotic A201A from Streptomyces capreolus.

A novel cosmid (pABC6.5) whose DNA insert from Streptomyces capreolus, the A201A antibiotic producer, overlaps the inserts of the previously reported pCAR11 and pCAR13 cosmids, has been isolated. These two latter cosmids were known to contain the aminonucleoside antibiotic A201A resistance determinants ard2 and ard1, respectively. Together, these three cosmids have permitted the identification of a DNA stretch of 19 kb between ard1 and ard2, which should comprise a large region of a putative A201A biosynthetic (ata) gene cluster. The sequence of the 7 kb upstream of ard1 towards ard2 reveals seven consecutive open reading frames: ataP3, ataP5, ataP4, ataP10, ataP7, ata12 and ataPKS1. Except for the last two, their deduced products present high similarities to an identical number of counterparts from the pur cluster of Streptomyces alboniger that were either known or proposed to be implicated in the biosynthesis of the N6,N6-dimethyl-3'-amino-3'-deoxyadenosine moiety of puromycin. Because A201A contains this chemical moiety, these ataP genes are most likely implicated in its biosynthesis. Accordingly, the ataP4, ataP5 and ataP10 genes complemented specific puromycin nonproducing Deltapur4, Deltapur5 and Deltapur10 mutants of S. alboniger, respectively. Amino acid sequence comparisons suggest that ata12 and ataPKS1 could be implicated in the biosynthesis of the d-rhamnose and alpha-p-coumaric acid moieties of A201A. Further sequencing of 2 kb of DNA downstream of ard1 has disclosed a region which might contain one end of the ata cluster.     

Growth under elevated atmospheric CO(2) concentration accelerates leaf senescence in sunflower (Helianthus annuus L.) plants

Some morphogenetic and metabolic processes were sensitive to a high atmospheric CO(2) concentration during sunflower primary leaf ontogeny. Young leaves of sunflower plants growing under elevated CO(2) concentration exhibited increased growth, as reflected by the high specific leaf mass referred to as dry weight in young leaves (16days). The content of photosynthetic pigments decreased with leaf development, especially in plants grown under elevated CO(2) concentrations, suggesting that high CO(2) accelerates chlorophyll degradation, and also possibly leaf senescence. Elevated CO(2) concentration increased the oxidative stress in sunflower plants by increasing H(2)O(2) levels and decreasing activity of antioxidant enzymes such as catalase and ascorbate peroxidase. The loss of plant defenses probably increases the concentration of reactive oxygen species in the chloroplast, decreasing the photosynthetic pigment content as a result. Elevated CO(2) concentration was found to boost photosynthetic CO(2) fixation, especially in young leaves. High CO(2) also increased the starch and soluble sugar contents (glucose and fructose) and the C/N ratio during sunflower primary leaf development. At the beginning of senescence, we observed a strong increase in the hexoses to sucrose ratio that was especially marked at high CO(2) concentration. These results indicate that elevated CO(2) concentration could promote leaf senescence in sunflower plants by affecting the soluble sugar levels, the C/N ratio and the oxidative status during leaf ontogeny. It is likely that systemic signals produced in plants grown with elevated CO(2), lead to early senescence and a higher oxidation state of the cells of these plant leaves.     

Hydrostatic pressure-induced changes in cellular protein synthesis

Hydrostatic pressure is a well-known effector of cellular protein synthesis. High continuous hydrostatic pressure inhibits protein synthesis in general. It has been known for a long time that 30S ribosomal subunit is associated with the effects of pressure on protein synthesis in prokaryotes, however, the mechanisms of action are still not completely understood. Our new data suggest that synthesis of eukaryotic elongation factor-2 (eEF-2) is decreased under 30 MPa continuous hydrostatic pressure. Thus, eEF-2 may have a role in the synthesis of pressure-regulated proteins in eukaryotic cells. The presence of pressure-sensitive proteins indicate that hydrostatic pressure can induce very specific responses in stressed cells. Accumulation of heat shock protein 70 and 90 beta occurs under high pressure, independent of the general inhibition of protein synthesis, although this response appears clearly weaker than during heat stress.     

Zur Kenntnis der Permeabilitätseigenschaften von Hippuris Vulgaris L

Zusammenfassung Die in den von Wahry (1936) für Luft- und Wasserblattzellen vonHippuris vulgaris L. vorgelegten Permeabilitätsreihen auftretenden Eigentümlichkeiten gaben den Anlaß zu einer näheren Untersuchung der Permeabilität dieser Zellen für einige Anelektrolyte.Die Untersuchungen wurden unter Befolgung der plasmometrischen Methode sowohl nach dem Total-als dem Partialdruckverfahren ausgeführt. Entgegen früheren Befunden zeigen die Ergebnisse der im Vorliegenden ausgeführten Versuche, daß die Permeabilitätseigenschaften sowohl der Palisadenzellen der Luftblätter als der entsprechenden Mesophyllzellen der Wasserblätter vonHippuris im Licht einander praktisch völlig gleichen. Ihre Permeabilitätsreihen gehören durchaus dem Normal-, d. h. demChara-Majanthemum-Typ an.Die zunächst lediglich als orientierend zu betrachtenden Dunkelversuche mit Harnstoff und Glyzerin ergaben folgendes. Längere Dunkelbehandlung (1–5 Tage) schien keinen Einfluß auf die Permeabilität der Wasserblattzellen zu haben, sondern diese belief sich sowohl im Licht als im Dunkeln in großen Zügen auf das gleiche. In diesem Punkt weichen also die Permeabilitätseigenschaften vonHippuris erheblich von denjenigen beiElodea undChara ab, deren Durchlässigkeit sich nach Järvenkylä bei fortgesetzter Dunkelbehandlung stetig erhöhte.Vorliegende Untersuchung wurde im Sommer 1938 im Botanischen Institut der Universität Helsinki ausgeführt, dessen Vorstand, Herrn Prof. Dr. K. Linkola ich hiermit bestens danke.Meinem Freund, Prof. Dr. R. Collander, an den ich mich auch bei der Ausführung dieser Arbeit jederzeit vertrauensvoll wenden durfte, sage ich meinen wärmsten Dank.     

Subregion-Specific Proteomic Signature in the Hippocampus for Recognition Processes in Adult Mice

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Polymorphism within the 3' flanking region of the bovine growth hormone receptor gene

Growth hormone receptor (GHR) has a major role in the regulation of growth hormone action, and thus, is an obvious candidate gene associated with milk production traits in mammals. The present authors have sequenced 273 bp of the 3' flanking region of the bovine GHR , and found three length variants and one base substitution polymorphism in this region. Allele frequencies of the length variants differ between Finnish native and commercial dairy cattle breeds. The chromosomal localization of GHR was confirmed to bovine chromosome 20 by synteny mapping and linkage analysis.     

Dingo Howls: The Content and Efficacy of a Long‐Range Vocal Signal

Signals are shaped through selective pressures impacting their information content (i.e. ‘what’ is conveyed) and their efficacy (i.e. ‘how’ is it conveyed). In the case of long‐range communication, a signal's structure should both convey information and allow for detection and discrimination despite the effects of environmental variability during propagation. Canid howls are an ideal example of a long‐range communication signal, although research has mostly focused on the relationships between howls’ acoustic characteristics and their potential information content in wolves, Canis lupus spp., and coyotes, Canis latrans. In this study, we quantified these relationships in another canid, the dingo, Canis familiaris dingo, to determine how their howls compare to that of other wild canids. We found that dingoes’ howls are individually distinctive and may convey gender cues. Playback experiments indicate that dingoes can perform class‐level recognition of familiar and unfamiliar individuals on the basis of vocalizations alone. These results mirror findings for other wild canids such as wolves and coyotes. Lastly, propagation experiments demonstrate that this signal's structure can permit long‐distance detectability and discriminability. We discuss our results in relation to the putative functions of canid howls and propose avenues for future research.